I just watched the DVD commentary on ItB, & JMS directly admits the G'Kar/Sheridan/Franklin plotline doesn't make a great deal of sense,

Of course, that isn't quite what JMS said on the commentary track:

"One of the dangers in doing a prequel is trying to make people who hadn't met before meet. And all the fans said, 'We never heard about Franklin having gone on this mission with Sheridan before. They never mentioned it in dialogue.' And I thought, well people don't normally tend to say when they met for the first time, and if it was a classified mission they wouldn't talk about it freely. So it is a bit of a stretch that he and G'Kar and Franklin would all meet at this point would meet, and never mention it again, ever. But I had to do something. It was two o'clock in the morning and I had to do something."

So while he does kid around about the situation, he also sets forth a perfectly good justification for doing what he did. That's hardly a "direct admission" that what he did doesn't make much sense. It is a little convenient, but it doesn't contradict anything we actually see and here on screen. And JMS's commentaries (like his script book intros) can't always be taken as gospel. His memory sometimes plays tricks on him. (On the ItB commentary he refers to TNT commissioning the TV movie after they picked the show up for its fifth season. In fact, ItB and Thirdspace were commissioned after TNT bought the rerun rights to the first four seasons, and the agreement to pick up year five didn't come until well after both had been shot. He also asks Mike Vejar if J. Patrick McCormack - Gen. Lefcourt - didn't also appear in the series in season 5 as a general who talks to Sheridan. McCormack, of course, played Lefcourt at the end of season 4 where he commanded the forces defending Mars in the Civil War. And in Volume 11 of the script books he confuses the U.S. Constitution and the Declaration of Independence.)